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Genome-wide association study

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https://www.readbyqxmd.com/read/27933755/maternal-pre-pregnancy-bmi-downregulates-neonatal-cord-blood-lep-methylation
#1
R Kadakia, Y Zheng, Z Zhang, W Zhang, L Hou, J L Josefson
BACKGROUND: Neonatal adiposity has many determinants and may be a risk factor for future obesity. Epigenetic regulation of metabolically important genes is a potential contributor. OBJECTIVES: The objective of the study is to determine whether methylation changes in the LEP gene in cord blood DNA are impacted by the maternal environment or affect neonatal adiposity measures. METHODS: A cross-sectional study of 114 full-term neonates born to healthy mothers with normal glucose tolerance was performed...
December 8, 2016: Pediatric Obesity
https://www.readbyqxmd.com/read/27933531/using-baseline-transcriptional-connectomes-in-rat-to-identify-genetic-pathways-associated-with-predisposition-to-complex-traits
#2
Laura Saba, Paula Hoffman, Boris Tabakoff
Although rat is a critical model organism in preclinical medications development, its use in systems genetics studies remains sparse. The PhenoGen database and website contain detailed information on the qualitative and quantitative aspects of the rat brain, liver, heart, and brown adipose transcriptome. This database has been generated using the HXB/BXH recombinant inbred panel and is being expanded to a hybrid rat diversity panel that includes many common inbred strains as well. By using such a panel, the PhenoGen project has created a renewable and cumulative resource for the rat genomics community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933530/visualization-of-results-from-systems-genetics-studies-in-chromosomal-context
#3
Karen Y Oróstica, Ricardo A Verdugo
This chapter describes methods currently available for visualizing results from systems genetics experiments. Here, we abstract from the statistical methods used for genetic mapping, which are dependent on the specific resource being used, i.e. F2, RILs, or outbred populations among others. We use a public dataset with results from a mouse eQTL experiment for three examples of visualization: genome-wide dot plots of marker-by-gene association, karyotype-like plots, and circos plots. Dot plots give a first overview of the results from eQTL mapping, allowing detecting genome-wide patterns of cis- and trans-genetic association to transcription level...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933525/expression-qtls-mapping-and-analysis-a-bayesian-perspective
#4
Martha Imprialou, Enrico Petretto, Leonardo Bottolo
The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27933404/genome-wide-high-content-sirna-screening-identifies-the-alzheimer-s-genetic-risk-factor-fermt2-as-a-major-modulator-of-app-metabolism
#5
Julien Chapuis, Amandine Flaig, Benjamin Grenier-Boley, Fanny Eysert, Virginie Pottiez, Gaspard Deloison, Alexandre Vandeputte, Anne-Marie Ayral, Tiago Mendes, Shruti Desai, Alison M Goate, John S K Kauwe, Florence Leroux, Adrien Herledan, Florie Demiautte, Charlotte Bauer, Fréderic Checler, Ronald C Petersen, Kaj Blennow, Henrik Zetterberg, Lennart Minthon, Vivianna M Van Deerlin, Virginia Man-Yee Lee, Leslie M Shaw, John Q Trojanowski, Marilyn Albert, Abhay Moghekar, Richard O'Brien, Elaine R Peskind, Nicolas Malmanche, Gerard D Schellenberg, Pierre Dourlen, Ok-Ryul Song, Carlos Cruchaga, Philippe Amouyel, Benoit Deprez, Priscille Brodin, Jean-Charles Lambert
Genome-wide association studies (GWASs) have identified 19 susceptibility loci for Alzheimer's disease (AD). However, understanding how these genes are involved in the pathophysiology of AD is one of the main challenges of the "post-GWAS" era. At least 123 genes are located within the 19 susceptibility loci; hence, a conventional approach (studying the genes one by one) would not be time- and cost-effective. We therefore developed a genome-wide, high-content siRNA screening approach and used it to assess the functional impact of gene under-expression on APP metabolism...
December 8, 2016: Acta Neuropathologica
https://www.readbyqxmd.com/read/27933312/the-genetics-and-epigenetics-of-ptsd-overview-recent-advances-and-future-directions
#6
Christina M Sheerin, Mackenzie J Lind, Kaitlin Bountress, Nicole R Nugent, Ananda B Amstadter
This paper provides a brief summary and commentary on the growing literature and current developments related to the genetic underpinnings of posttraumatic stress disorder (PTSD). We first briefly provide an overview of the behavioral genetic literature on PTSD, followed by a short synopsis of the substantial candidate gene literature with a focus on genes that have been meta-analyzed. We then discuss the genome-wide association studies (GWAS) that have been conducted, followed by an introduction to other molecular platforms used in PTSD genomic studies, such as epigenetic and expression approaches...
April 2017: Current Opinion in Psychology
https://www.readbyqxmd.com/read/27932479/progress-in-understanding-the-genetics-of-calcium-containing-nephrolithiasis
#7
John A Sayer
Renal stone disease is a frequent condition, causing a huge burden on health care systems globally. Calcium-based calculi account for around 75% of renal stone disease and the incidence of these calculi is increasing, suggesting environmental and dietary factors are acting upon a preexisting genetic background. The familial nature and significant heritability of stone disease is known, and recent genetic studies have successfully identified genes that may be involved in renal stone formation. The detection of monogenic causes of renal stone disease has been made more feasible by the use of high-throughput sequencing technologies and has also facilitated the discovery of novel monogenic causes of stone disease...
December 8, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27932233/schizophrenia-risk-alleles-and-neurodevelopmental-outcomes-in-childhood-a-population-based-cohort-study
#8
Lucy Riglin, Stephan Collishaw, Alexander Richards, Ajay K Thapar, Barbara Maughan, Michael C O'Donovan, Anita Thapar
BACKGROUND: Schizophrenia typically onsets after puberty but is often preceded by observable childhood neurodevelopmental impairments. Whether these childhood antecedents index genetic liability is unknown. We used polygenic risk scores derived from a patient discovery sample as indicators of the genetic liability of schizophrenia. Our aim was to identify the early childhood manifestations of this liability in a UK population-based cohort. METHODS: The study sample was the Avon Longitudinal Study of Parents and Children, a prospective population-based cohort study of 14701 children...
December 5, 2016: Lancet Psychiatry
https://www.readbyqxmd.com/read/27932076/single-nucleotide-polymorphisms-in-dna-glycosylases-from-function-to-disease
#9
Mariarosaria D'Errico, Eleonora Parlanti, Barbara Pascucci, Paola Fortini, Sara Baccarini, Valeria Simonelli, Eugenia Dogliotti
Oxidative stress is associated with a growing number of diseases that span from cancer to neurodegeneration. Most oxidatively induced DNA base lesions are repaired by the base excision repair (BER) pathway which involves the action of various DNA glycosylases. There are numerous genome wide studies attempting to associate single-nucleotide polymorphisms (SNPs) with predispositions to various types of disease; often, these common variants do not have significant alterations in their biochemical function and do not exhibit a convincing phenotype...
December 5, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27931260/prediction-of-breast-cancer-risk-based-on-common-genetic-variants-in-women-of-east-asian-ancestry
#10
Wanqing Wen, Xiao-Ou Shu, Xingyi Guo, Qiuyin Cai, Jirong Long, Manjeet K Bolla, Kyriaki Michailidou, Joe Dennis, Qin Wang, Yu-Tang Gao, Ying Zheng, Alison M Dunning, Montserrat García-Closas, Paul Brennan, Shou-Tung Chen, Ji-Yeob Choi, Mikael Hartman, Hidemi Ito, Artitaya Lophatananon, Keitaro Matsuo, Hui Miao, Kenneth Muir, Suleeporn Sangrajrang, Chen-Yang Shen, Soo H Teo, Chiu-Chen Tseng, Anna H Wu, Cheng Har Yip, Jacques Simard, Paul D P Pharoah, Per Hall, Daehee Kang, Yongbing Xiang, Douglas F Easton, Wei Zheng
BACKGROUND: Approximately 100 common breast cancer susceptibility alleles have been identified in genome-wide association studies (GWAS). The utility of these variants in breast cancer risk prediction models has not been evaluated adequately in women of Asian ancestry. METHODS: We evaluated 88 breast cancer risk variants that were identified previously by GWAS in 11,760 cases and 11,612 controls of Asian ancestry. SNPs confirmed to be associated with breast cancer risk in Asian women were used to construct a polygenic risk score (PRS)...
December 8, 2016: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/27931187/computational-strategies-for-alternative-single-step-bayesian-regression-models-with-large-numbers-of-genotyped-and-non-genotyped-animals
#11
Rohan L Fernando, Hao Cheng, Bruce L Golden, Dorian J Garrick
BACKGROUND: Two types of models have been used for single-step genomic prediction and genome-wide association studies that include phenotypes from both genotyped animals and their non-genotyped relatives. The two types are breeding value models (BVM) that fit breeding values explicitly and marker effects models (MEM) that express the breeding values in terms of the effects of observed or imputed genotypes. MEM can accommodate a wider class of analyses, including variable selection or mixture model analyses...
December 8, 2016: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/27930647/allelic-variation-in-cxcl16-determines-cd3-t-lymphocyte-susceptibility-to-equine-arteritis-virus-infection-and-establishment-of-long-term-carrier-state-in-the-stallion
#12
Sanjay Sarkar, Ernest Bailey, Yun Young Go, R Frank Cook, Ted Kalbfleisch, John Eberth, R Lakshman Chelvarajan, Kathleen M Shuck, Sergey Artiushin, Peter J Timoney, Udeni B R Balasuriya
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of horses and other equid species. Following natural infection, 10-70% of the infected stallions can become persistently infected and continue to shed EAV in their semen for periods ranging from several months to life. Recently, we reported that some stallions possess a subpopulation(s) of CD3+ T lymphocytes that are susceptible to in vitro EAV infection and that this phenotypic trait is associated with long-term carrier status following exposure to the virus...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27930307/cosmc-is-an-x-linked-inflammatory-bowel-disease-risk-gene-that-spatially-regulates-gut-microbiota-and-contributes-to-sex-specific-risk
#13
Matthew R Kudelka, Benjamin H Hinrichs, Trevor Darby, Carlos S Moreno, Hikaru Nishio, Christopher E Cutler, Jianmei Wang, Huixia Wu, Junwei Zeng, Yingchun Wang, Tongzhong Ju, Sean R Stowell, Asma Nusrat, Rheinallt M Jones, Andrew S Neish, Richard D Cummings
Inflammatory bowel disease (IBD) results from aberrant immune stimulation against a dysbiotic mucosal but relatively preserved luminal microbiota and preferentially affects males in early onset disease. However, factors contributing to sex-specific risk and the pattern of dysbiosis are largely unexplored. Core 1 β3GalT-specific molecular chaperone (Cosmc), which encodes an X-linked chaperone important for glycocalyx formation, was recently identified as an IBD risk factor by genome-wide association study. We deleted Cosmc in mouse intestinal epithelial cells (IECs) and found marked reduction of microbiota diversity in progression from the proximal to the distal gut mucosa, but not in the overlying lumen, as seen in IBD...
December 7, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27929136/an-integrated-genomic-approach-for-the-study-of-mandibular-prognathism-in-the-european-seabass-dicentrarchus-labrax
#14
Massimiliano Babbucci, Serena Ferraresso, Marianna Pauletto, Rafaella Franch, Chiara Papetti, Tomaso Patarnello, Paolo Carnier, Luca Bargelloni
Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27929092/the-known-genetic-loci-for-telomere-length-may-be-involved-in-the-modification-of-telomeres-length-after-birth
#15
Qiao Weng, Jiangbo Du, Fei Yu, Tongtong Huang, Mengxi Chen, Hong Lv, Hongxia Ma, Zhibin Hu, Guangfu Jin, Yali Hu, Hongbing Shen
Telomere length varies considerably among individuals. It is highly heritable and decreases with ageing or ageing related diseases. Recently, genome-wide association studies (GWAS) have identified several genetic loci associated with telomere length in adults. However, it is unclear whether these loci represent the genetic basis of telomere length or determine the individual susceptibility to shortening during growth process. Using DNA extracted from peripheral and cord blood of 444 mother-newborn pairs from a Chinese population, we measured relative telomere length (RTL) and genotyped eight known telomere length related variants that were initially identified in populations of European descent...
December 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27928975/assessing-causality-in-associations-between-cannabis-use-and-schizophrenia-risk-a-two-sample-mendelian-randomization-study
#16
S H Gage, H J Jones, S Burgess, J Bowden, G Davey Smith, S Zammit, M R Munafò
BACKGROUND: Observational associations between cannabis and schizophrenia are well documented, but ascertaining causation is more challenging. We used Mendelian randomization (MR), utilizing publicly available data as a method for ascertaining causation from observational data. METHOD: We performed bi-directional two-sample MR using summary-level genome-wide data from the International Cannabis Consortium (ICC) and the Psychiatric Genomics Consortium (PGC2). Single nucleotide polymorphisms (SNPs) associated with cannabis initiation (p < 10-5) and schizophrenia (p < 5 × 10-8) were combined using an inverse-variance-weighted fixed-effects approach...
December 8, 2016: Psychological Medicine
https://www.readbyqxmd.com/read/27928162/role-of-mirnas-in-the-pathogenesis-and-susceptibility-of-diabetes-mellitus
#17
REVIEW
Naoko Hashimoto, Tomoaki Tanaka
MicroRNAs (miRNAs) are noncoding RNAs of ~22 nucleotides that regulate gene expression post-transcriptionally by binding to the 3' untranslated region of messenger RNA (mRNAs), resulting in inhibition of translation or mRNA degradation. miRNAs have a key role in fine-tuning cellular functions such as proliferation, differentiation and apoptosis, and they are involved in carcinogenesis, glucose homeostasis, inflammation and other biological processes. In this review, we focus on the role of miRNAs in the pathophysiology of the metabolic disease and diabetes mellitus, the hallmark of which is hyperglycemia caused by defective insulin secretion and/or action...
December 8, 2016: Journal of Human Genetics
https://www.readbyqxmd.com/read/27928018/expression-of-the-antisense-to-latency-transcript-long-noncoding-rna-in-kaposi-s-sarcoma-associated-herpesvirus
#18
Jason M Schifano, Kathleen Corcoran, Hemant Kelkar, Dirk P Dittmer
: The regulation of latency is central to herpesvirus biology. Recent transcriptome-wide surveys have uncovered evidence for promiscuous transcription across the entirety of the Kaposi sarcoma-associated herpesvirus genome and postulated the existence of multiple viral long noncoding RNAs (lncRNAs). NextGen sequencing studies are highly dependent on the specific experimental approach and particular algorithms of analysis, and therefore benefit from independent confirmation of the results...
December 7, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27927781/genetic-variants-associated-with-circulating-parathyroid-hormone
#19
Cassianne Robinson-Cohen, Pamela L Lutsey, Marcus E Kleber, Carrie M Nielson, Braxton D Mitchell, Joshua C Bis, Karen M Eny, Laura Portas, Joel Eriksson, Mattias Lorentzon, Daniel L Koller, Yuri Milaneschi, Alexander Teumer, Stefan Pilz, Maria Nethander, Elizabeth Selvin, Weihong Tang, Lu-Chen Weng, Hoi Suen Wong, Dongbing Lai, Munro Peacock, Anke Hannemann, Uwe Völker, Georg Homuth, Matthias Nauk, Federico Murgia, Jack W Pattee, Eric Orwoll, Joseph M Zmuda, Jose Antonio Riancho, Myles Wolf, Frances Williams, Brenda Penninx, Michael J Econs, Kathleen A Ryan, Claes Ohlsson, Andrew D Paterson, Bruce M Psaty, David S Siscovick, Jerome I Rotter, Mario Pirastu, Elizabeth Streeten, Winfried März, Caroline Fox, Josef Coresh, Henri Wallaschofski, James S Pankow, Ian H de Boer, Bryan Kestenbaum
Parathyroid hormone (PTH) is a primary calcium regulatory hormone. Elevated serum PTH concentrations in primary and secondary hyperparathyroidism have been associated with bone disease, hypertension, and in some studies, cardiovascular mortality. Genetic causes of variation in circulating PTH concentrations are incompletely understood. We performed a genome-wide association study of serum PTH concentrations among 29,155 participants of European ancestry from 13 cohort studies (n=22,653 and n=6502 in discovery and replication analyses, respectively)...
December 7, 2016: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/27927641/genetic-architecture-distinguishes-systemic-juvenile-idiopathic-arthritis-from-other-forms-of-juvenile-idiopathic-arthritis-clinical-and-therapeutic-implications
#20
Michael J Ombrello, Victoria L Arthur, Elaine F Remmers, Anne Hinks, Ioanna Tachmazidou, Alexei A Grom, Dirk Foell, Alberto Martini, Marco Gattorno, Seza Özen, Sampath Prahalad, Andrew S Zeft, John F Bohnsack, Norman T Ilowite, Elizabeth D Mellins, Ricardo Russo, Claudio Len, Maria Odete E Hilario, Sheila Oliveira, Rae S M Yeung, Alan M Rosenberg, Lucy R Wedderburn, Jordi Anton, Johannes-Peter Haas, Angela Rosen-Wolff, Kirsten Minden, Klaus Tenbrock, Erkan Demirkaya, Joanna Cobb, Elizabeth Baskin, Sara Signa, Emily Shuldiner, Richard H Duerr, Jean-Paul Achkar, M Ilyas Kamboh, Kenneth M Kaufman, Leah C Kottyan, Dalila Pinto, Stephen W Scherer, Marta E Alarcón-Riquelme, Elisa Docampo, Xavier Estivill, Ahmet Gül, Carl D Langefeld, Susan Thompson, Eleftheria Zeggini, Daniel L Kastner, Patricia Woo, Wendy Thomson
OBJECTIVES: Juvenile idiopathic arthritis (JIA) is a heterogeneous group of conditions unified by the presence of chronic childhood arthritis without an identifiable cause. Systemic JIA (sJIA) is a rare form of JIA characterised by systemic inflammation. sJIA is distinguished from other forms of JIA by unique clinical features and treatment responses that are similar to autoinflammatory diseases. However, approximately half of children with sJIA develop destructive, long-standing arthritis that appears similar to other forms of JIA...
December 7, 2016: Annals of the Rheumatic Diseases
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